How structural biology transformed studies of transcription regulation

Wolberger, Cynthia

doi:10.1016/j.jbc.2021.100741

Cited by 25 publications

(12 citation statements)

References 87 publications

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“…Although CAF- 1 prefers to bind to tetrasome-length DNA (Luger et al, 1997; Donham, Scorgie, and Churchill, 2011), the KER SAH is capable of binding to DNA as short as 20 bp, which is typical of many DBDs. Many alpha helical DNA binding motifs, including leucine zippers and helix-loop-helix motifs, bind across the DNA within the major groove (Luscombe et al, 2000; Wolberger, 2021; Churchill and Travers, 1991). In contrast, long helices that lie parallel to the DNA exist in chromatin remodelers, such as the HSA and post-HSA domains in the actin related proteins (Arp4 and Arp8) of INO80 (Knoll et al, 2018; Baker et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

A novel Single Alpha-Helix-DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function

Rosas

Aguilar

Arslanovic

et al. 2022

Preprint

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The histone chaperone chromatin assembly factor 1 (CAF-1) deposits nascent histone H3/H4 dimers onto newly replicated DNA forming the central core of the nucleosome known as the tetrasome. How CAF-1 ensures there is sufficient space for the assembly of tetrasomes remains unknown. Structural and biophysical characterization of the lysine/glutamic acid/arginine-rich (KER) region of CAF-1 revealed a 128 Å single alpha helix (SAH) motif with unprecedented DNA binding properties. Distinct KER sequence features and length of the SAH drive the selectivity of CAF-1 for tetrasome-length DNA and facilitate function in budding yeast. In vivo, the KER cooperates with the DNA-binding winged helix domain in CAF-1 to overcome DNA damage sensitivity and maintain silencing of gene expression. We propose that the KER SAH links functional domains within CAF-1 with structural precision, acting as a DNA binding spacer element during chromatin assembly.

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Section: Discussionmentioning

confidence: 99%

A novel Single Alpha-Helix-DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function

Rosas

Aguilar

Arslanovic

et al. 2022

Preprint

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“…An analysis of the structures deposited on the PDB for ten different protein families suggests that the number of structures and the preference for a particular technique for its resolution is not uniform across these families [104] (Figure 3A-J). As expected, X-ray crys-tallography is by far the most frequently used technique for the structural characterization of proteins, notably surpassing NMR and Cryo-EM in the total number of structures solved by these techniques.…”

Section: Structural Characterization Of the Different Allosteric Statesmentioning

confidence: 99%

Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization

Diez

Juncos

Dujovne

et al. 2022

IJMS

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The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.

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“…Notably, the major groove is almost non-existent, while the minor groove is narrow. Tracts alternating dinucleotide repeating purine-pyrimidine or pyrimidine-purine (APP) sequences are known to adopt the left-handed conformation [ 16 , 17 ], and are over-represented in higher eukaryotes. In fact, GpC repeats, also named “CpG islands”, show a strong attitude to crystallizing as a Z-structure [ 18 ].…”

Section: Overview Of Nucleic Acidsmentioning

confidence: 99%

DNA Studies: Latest Spectroscopic and Structural Approaches

et al. 2021

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This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

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How structural biology transformed studies of transcription regulation

Cited by 25 publications

References 87 publications

A novel Single Alpha-Helix-DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function

A novel Single Alpha-Helix-DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function

Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization

DNA Studies: Latest Spectroscopic and Structural Approaches

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